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ShareScore release 0.9.0
Dataset results
19 results for “short-read sequencing”
Data from: Improved genome assembly of the whiteleg shrimp Penaeus (Litopenaeus) vannamei using long- and short-read sequences from public databases
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Data from: Microhaplotypes provide increased power from short-read DNA sequences for relationship inference
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Next-generation sequencing of newborn screening genes: The accuracy of short-read mapping
<p>We examine the effect of high homology genomic regions on the mapping of genes related to newborn screening while taking different read lengths and patient's ethnic background into consideration.</p>
Data from Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches
<p><strong>Background</strong></p> <p>The application of reduced metagenomic sequencing approaches holds promise as a middle ground between targeted amplicon sequencing and whole metagenome sequencing approaches but has not been widely adopted as a technique. A major barrier to adoption is the lack of read simulation software built to handle characteristic features of these novel approaches. Reduced metagenomic sequencing (RMS) produces unique patterns of fragmentation per genome that are sensitive to restriction enzyme choice, and the non-uniform size selection of these fragments may introduce novel challenges to taxonomic assignment as well as relative abundance estimates.</p> <p><strong>Results</strong></p> <p>Through the development and application of simulation software, readsynth, we compare simulated metagenomic sequencing libraries with existing RMS data to assess the influence of multiple library preparation and sequencing steps on downstream analytical results. Based on read depth per position, readsynth achieved 0.79 Pearson's correlation and 0.94 Spearman's correlation to these benchmarks. Application of a novel estimation approach, fixed length taxonomic ratios, improved quantification accuracy of simulated human gut microbial communities when compared to estimates of mean or median coverage.</p> <p><strong>Conclusions</strong></p> <p>We investigate the possible strengths and weaknesses of applying the RMS technique to profiling microbial communities via simulations with readsynth. The choice of restriction enzymes and size selection steps in library prep are non-trivial decisions that bias downstream profiling and quantification. The simulations investigated in this study illustrate the possible limits of preparing metagenomic libraries with a reduced representation sequencing approach, but also allow for the development of strategies for producing and handling the sequence data produced by this promising application.</p>
A HKU5-related Coronavirus identified and assembled from Short-Read sequencing data of Gossypium Barbadense
<p>This is the complete annotated genome of the Merbecovirus identified from Gossypium Barbadense sequencing data, <a href="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR5885860">SRR5885860</a></p>
Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation
<p>SNV of 23 parental barley inbreds of the double round robin population (DRR) (<a href="https://doi.org/10.1111/pbi.13746">https://doi.org/10.1111/pbi.13746</a>) used in the publication "Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation". SV, INDELs, and additional data are available via figshare (https://doi.org/10.6084/m9.figshare.16802473).</p>
Comprehensive identification of pathogenic variants in retinoblastoma by long- and short-read sequencing
<p>Retinoblastoma (RB) is the most common intraocular malignancy in childhood. The causal variants in RB are mostly characterized by previously used short-read sequencing (SRS) analysis, which has technical limitations in identifying structural variants (SVs) and phasing information. Long-read sequencing (LRS) technology has significant advantages over SRS in detecting SVs, phased genetic variants, and methylation. In this study, we comprehensively characterized the genetic landscape of RB using combinatorial LRS and SRS of 16 RB tumors and 16 matched blood samples. We detected a total of 232 somatic SVs, with an average of 14.5 SVs per sample across the cohort. We identified 20 distinct pathogenic variants, including <span>three</span> novel small variants and <span>five</span> <span>somatic</span> SVs. Furthermore, our analysis shows that the vast majority (93.8%) of <em>RB1</em>-disrupted patients fit the two-hit hypothesis through diverse types, including the biallelic hypermethylated promoter as well as small and large compound heterozygous mutations which were missing in SRS analysis. By constructing the evolutionary history of all genetic variants, we reveal the evolution trends that <em>RB1</em> disruption early and followed by copy number changes, including amplifications of Chr2p, and deletions of Chr16q, during RB tumorigenesis. Altogether, we characterize the comprehensive genetic landscape of RB, providing novel insights into the genetic alterations and mechanisms contributing to RB initiation and development. Our work also establishes a framework to analyze genomic landscape of cancers based on LRS data. <br><br>We took IGV screenshots of SV and SNV/indels. The IGV naming conventions for SV is: sample name, chromosome 1, start, chromosome 2, end, SV type, SV length, SV breakpoint. The IGV naming convention for SNV/indels is: sample name, chromosome, position, reference allele, alternate allele.</p>
Assessing reproduciblity of Inherited Variants Detected with Short-read Whole Genome Sequencing
<p>This dataset is part of the following study:</p> <p><a href="https://www.fda.gov/science-research/bioinformatics-tools/microarraysequencing-quality-control-maqcseqc">https://www.fda.gov/science-research/bioinformatics-tools/microarraysequencing-quality-control-maqcseqc</a></p> <p>The raw sequencing data can be downloaded from SRA:</p> <p><a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA723125">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA723125</a></p> <p>and NODE:</p> <p><a href="https://www.biosino.org/node/project/detail/OEP0018966">https://www.biosino.org/node/project/detail/OEP0018966</a></p>
Data from Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches
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Analysis of Public Short-Read RNA-Sequencing Data: PRJNA543316
<p><strong><span>PRJNA543316</span></strong></p> <p><span>Metformin is a front-line drug in the treatment of type-2 diabetes mellitus (T2DM). In addition to its antigluconeogenic and insulin-sensitizing properties, it has emerged as a potent inhibitor of the inflammatory response of macrophages. Specifically, metformin has been shown to reduce transcript levels of Il1b, the gene encoding the pro-inflammatory cytokine interleukin (IL)-1b, during long-term exposure of macrophages to the bacterial cell-wall component lipopolysaccharide (LPS). However, the extent to which metformin affects the early transcriptional response to LPS has never been investigated. Here, we show that metformin affects transcript levels of a large yet selective subset of LPS-responsive genes after only two hours of LPS exposure, mostly counteracting the effect of LPS rather than enhancing it. The affected genes are implicated in a variety of biological functions, in particular cellular movement and trafficking. Intriguingly, metformin affects transcript levels of Il1b at this early time point as well, but through a molecular mechanism fundamentally different from the regulation observed after longer exposure. While down-regulation of Il1b by metformin during the late stages of the LPS response has been shown to rely on stabilization of hypoxia-inducible factor (HIF)-1α and production of IL-10, Il1b inhibition at the early stage requires AMP-activated protein kinase (AMPK) activation but is independent of HIF-1α and IL-10. These results reveal an unexpected complexity in the anti-inflammatory properties of metformin and demonstrate that Il1b is down-regulated by distinct mechanisms in the early and late stages of the LPS response. Overall design: Bone-marrow-derived macrophages from WT C57Bl/6 mice were either left untreated, stimulated with 100 ng/ml LPS for 2 h or pretreated with 5 mM metformin for 6 h and then stimulated with 100 ng/ml LPS for 2 h.</span></p> <p><span>Pipeline: FastQ -> FastQC -> fastp -> STAR -> samtools -> multiQC</span></p>
Dissecting long non-coding RNAs derived from microRNA genes in hematopoiesis (Illumina short-read sequencing)
GEO Series GSE180565. Homo sapiens. 61 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other.
Long- and short-read RNA sequencing from five reproductive organs of boar.
GEO Series GSE230506. Sus scrofa. 70 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Efficient Yeast ChIP-Seq using Multiplex Short-Read DNA Sequencing
GEO Series GSE13322. Saccharomyces cerevisiae. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Integrated long- and short-read single-cell RNA-sequencing
GEO Series GSE166709. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Data from: Haplotype-phased synthetic long reads from short-read sequencing
Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucleic acid molecules up to 11.6 kilobases in length from short (150-bp) reads. We show that our method can construct 99.97%-accurate synthetic reads from bacterial, plant, and animal genomic samples, full-length mRNA sequences from human cancer cell lines, and individual HIV env gene variants from a mixture. The preparation of multiple samples can be multiplexed into a single tube, further reducing effort and cost relative to competing approaches. Our approach generates sequencing libraries in three days from less than one microgram of DNA in a single-tube format without custom equipment or specialized expertise.
Mitochondrial Diseases - Long-read Genome and Transcriptome Sequencing in Cases Unresolved After Short-read Genomics
ClinicalTrials.gov study NCT03962452. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Haplotype-phased synthetic long reads from short-read sequencing
Open the record for dataset details and reuse information.
Long-read RNA sequencing reveals synaptic genes with differential isoform usage in schizophrenia [short-read RNAseq ]
GEO Series GSE282552. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Short-read nascent RNA sequencing from S. pombe
GEO Series GSE104680. Schizosaccharomyces pombe. 14 samples. Type: Expression profiling by high throughput sequencing; Other.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.